Combine multiple output directories

CWL Questions
1

Hi,

is it possible to combine multiple outputs of type directory from different tools running in parallel into a single directory? I get this error when trying:

Composer: {"status": "COMPLETED", "stepId": "root.mINFOe[0m [step astrolabe_5"}
e[1;30mERRORe[0m e[31m[workflow ] Cannot collect workflow output: Workflow contains multiple inbound links to a single parameter but MultipleInputFeatureRequirement is not declared.e[0m

class: Workflow
cwlVersion: v1.0
id: astrolabe_full
label: astrolabe-full
$namespaces:
  sbg: 'https://www.sevenbridges.com/'
requirements:
  MultipleInputFeatureRequirement: {}
inputs:
  - id: rosbag
    type: File
    'sbg:x': -60
    'sbg:y': -50
  - id: json_file
    type:
      - 'null'
      - File
      - type: array
        items: File
    'sbg:x': -51
    'sbg:y': 186
outputs:
  - id: output_data_dir
    outputSource:
      - astrolabe_2/output_data_dir
      - astrolabe_1/output_data_dir
    type:
      - Directory
      - type: array
        items: Directory
    linkMerge: merge_flattened
    'sbg:x': 740.9171142578125
    'sbg:y': 54
steps:
  - id: astrolabe_1
    in:
      - id: input_data_dir
        source: astrolabe/output-data-directory
      - id: transform_plugin
        default: events_data
    out:
      - id: output_data_dir
    run: ../astrolabe-transform.cwl
    label: astrolabe transform
    'sbg:x': 444.9171447753906
    'sbg:y': 108.5
  - id: astrolabe_2
    in:
      - id: input_data_dir
        source: astrolabe/output-data-directory
      - id: transform_plugin
        default: console_out
    out:
      - id: output_data_dir
    run: ../astrolabe-transform.cwl
    label: astrolabe transform
    'sbg:x': 443
    'sbg:y': -42
  - id: astrolabe
    in:
      - id: extract-plugin
        default: rosbag
      - id: rosbag
        source: rosbag
      - id: json_file
        source:
          - json_file
    out:
      - id: output-data-directory
    run: ../astrolabe-extract.cwl
    label: astrolabe extract rosbag
    'sbg:x': 143.796875
    'sbg:y': 47.5

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image.png977×347 40.9 KB

2

Hi @FJ_Sanchez,

My guess would it should localise the directories to two different places, and then the value of your variable of directory[] would just be two paths pointing to each directory.

Have you tried running this on CWLTool (by default Rabix Composer uses bunny I believe), looks like you correctly include the MultipleInputFeatureRequirement which means it shouldn’t throw the error it did.